NAR Paper

Overivew

The Nucleic Acids Research (NAR) paper in the annual database issue presents to the world our latest data and software developments. There is a long history of different authors and this page provides a place to find resources regarding the process.

NAR provides many instructions for writing the paper, important to review. A template is provided at this link.

NAR provides a Checklist and a Revision Instructions Sheet after you submit your paper, but review them first to help you write your first drafts better.

Presentations

• Cath wrote the paper in 2016 (2017 Update is submitted in Sept. 2016) and put together a "Reflections: Writing the NAR" presentation with slides available here.
• Jairo wrote the paper in 2020 and put together a "Writing the NAR Update" presentation with slides available here.
• BrianL wrote the paper in 2021 and put together a "Writing the NAR Paper" slide deck available here.

Tips

Cath's tips seem pretty timeless for any potential NAR author.

Schedule

Here is a model reverse timeline schedule from Memorial Day to Labor Day. Note how it takes into account planned vacations to frame things in a realistic context.

Week end 9/Z: (9/15 Due)
Week end 9/Z:  (Labor Day Holiday)
Week end 9/Z:
Week end 8/Y: FINALIZED DRAFT TO ENTIRE TEAM
Week end 8/Y: 
Week end 8/Y:  DRAFT2  REVIEW TEAM_2
Week end 8/Y:  (Vacation_2 if planned 8/A-8/B)
Week end 7/X:  DRAFT1    REVIEW TEAM_1
Week end 7/X:  
Week end 7/X: (Vacation_1 if planned 7/A-7/B)
Week end 7/X:  (4th of July Holiday)
Week end 7/X:  (Week of Memorial Day Holiday)

Outline

Here is a conceptual skeleton outline to help launch things.

ABSTRACT
INTRODUCTION
NEW DATA IN THE GENOME BROWSER
-subsection 1
-subsection 2 
-subsection 3 - as makes sense
NEW SOFTWARE FEATURES IN THE GENOME BROWSER
-subsection 1
-subsection 2
-subsection 3 - as makes sense
FUTURE PLANS
OUTREACH AND CONTACT INFORMATION
ACKNOWLEDGEMENTS
FUNDING
REFERENCES

References

There is an internal wikipage about using Zotero that can be helpful for references. It turns out you don't want to use the "NAR Web Server Issue" in Zotero style that adds URLs.

Images

If you have screenshots will likely need to correct the DPI (as mentioned in Cath's overview). One tool to try is GIMP (https://www.gimp.org/) to do the conversion. Another is online at https://convert.town/image-dpi.

If you upload your images to Dev you can run a program that is already installed called imagemagick invoked with the "convert" command to take an input "image" and output a "resultImage" to 300dpi and in the process make a very nice resample so it looks the best possible: convert -units PixelsPerInch image -resample 300 resultimage

Real example commands involving 7 image files called FIGURE_#.png with results placed in a created now300DPI directory:

scp FIGURE_* login@hgwdev.gi.ucsc.edu:/cluster/home/userName/public_html/location
for i in {1..7}; do convert -units PixelsPerInch FIGURE_$i.png -resample 300 now300DPI/FIGURE_$i.png; done

Previous NAR papers

2021 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779060/
2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145642/
2019 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323953/
2018 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753355/
2017 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210591/
2016 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702902/
2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971
2014 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964947
2013 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531082
2012 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245018
2011 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242726
2010 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808870

Referees (aka Reviewers)

Cath's PDF presentation is chalk full of resources to google docs. We have been recording the referees used here, it would be kind to list the ones you use. Email the group to ask for ideas of good names (some people have recently acted as a referee on a paper for others in the field and they might suggest new names).

License charge

To publish the paper in the past a PO (Purchase Order) was required, you want to contact GI Finance (genomics.finance@ucsc.edu) to communicate about the need to pay for the publication. In 2021 the PO process changed. In the past we have used the "CC BY" which is explained at NAR: The Creative Commons Attribution licence (CC BY) is the most liberal of the Creative Commons licences and allows for unrestricted reuse, even commercial, as long as the author is credited for their original creation. While Oxford Journals Author Services allows you to pay online using a credit card, our grant and finance pays for this transaction (don't ask ProCard holder for the Browser credit card number). The old PO way for this charge was $1,385 USD in 2016 and $3,800 USD in 2020, so don't be surprised if it is a lot more in the future. In 2021 finance informed BrianL that in stead of a PO we can "Just send the invoice to [Finance] and I [Linda Knipe] will submit for direct payment to the vendor." This should make things easier as the PO process was a bit complicated previously.